scriptutils.helpers
Module Contents
Functions
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Test if a given URI is in the ontology (effectively an exception-checking wrapper around get_term_by_uri) |
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Remove extra prefixes common in insert names |
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Generate a dictionary of sanitized names for elements in a synthesis order that are |
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Shorten a name by lopping off front chunks, breaking it at underscores if possible |
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If the component is a vector, peel it open to find the sub-component that is not the vector portion |
- has_SO_uri(uri: str) bool
Test if a given URI is in the ontology (effectively an exception-checking wrapper around get_term_by_uri)
- Parameters
ontology – Ontology to check for term containment
str – URI to look up
- Returns
true if this is a URI in the
- remove_duplicate_prefix(name: str) str
Remove extra prefixes common in insert names TODO: remove on resolution of https://github.com/iGEM-Engineering/iGEM-distribution/issues/161 :param name: name to sanitize :return sanitized name
- sanitize_identifiers_for_synthesis(components: collections.Iterable[sbol3.Component], max_len: int = 32) dict[sbol3.Component, str]
Generate a dictionary of sanitized names for elements in a synthesis order that are acceptable for a synthesis provides and contain no duplicates.
- Parameters
components – Collection of components to generate sanitized names for
max_len – maximum length of a sanitized name
- Returns
dictionary mapping each insert to its sanitized name
- truncate_by_underscores(name: str, max_len: int) str
Shorten a name by lopping off front chunks, breaking it at underscores if possible
- Parameters
name – name to truncate
max_len – cutoff size
- Returns
truncated name
- vector_to_insert(component: sbol3.Component) sbol3.Component
If the component is a vector, peel it open to find the sub-component that is not the vector portion If the component is not a vector, return it directly Throws a ValueError if the component is a vector but does not have precisely one insert
- Parameters
component – SBOL3 component to extract from
- Returns
component if not vector; otherwise the vector